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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.24.1

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-10-17, 06:43 AEDT based on data in: /data/group/frankslab/project/LFlorence/NitrogenDeposition-AusForests/am_fungi/data/primers_trimmed


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        General Statistics

        Showing 256/256 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        m10_R1
        94.7%
        46%
        284bp
        0.0M
        m10_R2
        84.8%
        44%
        274bp
        0.0M
        m11_R1
        92.3%
        45%
        284bp
        0.1M
        m11_R2
        83.7%
        44%
        274bp
        0.1M
        m12_R1
        92.3%
        45%
        284bp
        0.0M
        m12_R2
        76.8%
        44%
        274bp
        0.0M
        m13_R1
        97.1%
        46%
        284bp
        0.1M
        m13_R2
        88.7%
        44%
        274bp
        0.1M
        m14_R1
        92.0%
        44%
        284bp
        0.0M
        m14_R2
        82.3%
        42%
        274bp
        0.0M
        m15_R1
        92.0%
        44%
        284bp
        0.0M
        m15_R2
        82.4%
        42%
        274bp
        0.0M
        m16_R1
        90.2%
        46%
        284bp
        0.0M
        m16_R2
        78.3%
        44%
        274bp
        0.0M
        m17_R1
        94.1%
        47%
        284bp
        0.0M
        m17_R2
        86.9%
        44%
        274bp
        0.0M
        m18_R1
        92.6%
        46%
        284bp
        0.1M
        m18_R2
        83.0%
        44%
        274bp
        0.1M
        m19_R1
        94.9%
        47%
        284bp
        0.1M
        m19_R2
        86.9%
        44%
        274bp
        0.1M
        m1_R1
        94.9%
        47%
        284bp
        0.1M
        m1_R2
        88.1%
        44%
        274bp
        0.1M
        m20_R1
        89.8%
        46%
        284bp
        0.1M
        m20_R2
        78.6%
        44%
        274bp
        0.1M
        m21_R1
        93.7%
        43%
        284bp
        0.1M
        m21_R2
        83.7%
        41%
        274bp
        0.1M
        m22_R1
        90.8%
        45%
        284bp
        0.0M
        m22_R2
        81.7%
        44%
        274bp
        0.0M
        m23_R1
        96.5%
        46%
        284bp
        0.1M
        m23_R2
        85.7%
        44%
        274bp
        0.1M
        m24_R1
        94.0%
        45%
        284bp
        0.0M
        m24_R2
        84.0%
        44%
        274bp
        0.0M
        m25_R1
        97.7%
        46%
        284bp
        0.7M
        m25_R2
        92.0%
        43%
        274bp
        0.7M
        m26_R1
        92.2%
        46%
        284bp
        0.0M
        m26_R2
        82.2%
        44%
        274bp
        0.0M
        m27_R1
        95.4%
        46%
        284bp
        0.1M
        m27_R2
        87.4%
        43%
        274bp
        0.1M
        m28_R1
        95.3%
        45%
        284bp
        0.1M
        m28_R2
        85.2%
        43%
        274bp
        0.1M
        m29_R1
        94.3%
        46%
        284bp
        0.1M
        m29_R2
        87.2%
        45%
        274bp
        0.1M
        m2_R1
        88.7%
        46%
        284bp
        0.1M
        m2_R2
        80.1%
        44%
        274bp
        0.1M
        m31_R1
        92.4%
        45%
        284bp
        0.0M
        m31_R2
        82.1%
        42%
        274bp
        0.0M
        m32_R1
        94.9%
        45%
        284bp
        0.3M
        m32_R2
        89.2%
        43%
        274bp
        0.3M
        m33_R1
        90.5%
        47%
        284bp
        0.0M
        m33_R2
        76.4%
        44%
        274bp
        0.0M
        m34_R1
        96.1%
        45%
        284bp
        0.3M
        m34_R2
        88.4%
        44%
        274bp
        0.3M
        m35_R1
        93.3%
        48%
        284bp
        0.1M
        m35_R2
        86.1%
        44%
        274bp
        0.1M
        m36_R1
        92.7%
        47%
        284bp
        0.3M
        m36_R2
        84.9%
        43%
        274bp
        0.3M
        m37_R1
        92.9%
        46%
        284bp
        0.1M
        m37_R2
        84.6%
        44%
        274bp
        0.1M
        m38_R1
        91.1%
        47%
        284bp
        0.0M
        m38_R2
        81.2%
        45%
        274bp
        0.0M
        m39_R1
        97.6%
        45%
        284bp
        1.3M
        m39_R2
        94.4%
        44%
        274bp
        1.3M
        m3_R1
        90.3%
        46%
        284bp
        0.1M
        m3_R2
        82.6%
        44%
        274bp
        0.1M
        m40_R1
        96.9%
        46%
        284bp
        1.1M
        m40_R2
        91.8%
        43%
        274bp
        1.1M
        m41_R1
        98.2%
        47%
        284bp
        1.3M
        m41_R2
        93.6%
        44%
        274bp
        1.3M
        m42_R1
        85.7%
        46%
        284bp
        0.0M
        m42_R2
        73.3%
        44%
        274bp
        0.0M
        m43_R1
        94.9%
        48%
        284bp
        0.1M
        m43_R2
        87.1%
        44%
        274bp
        0.1M
        m44_R1
        90.1%
        46%
        284bp
        0.1M
        m44_R2
        80.8%
        43%
        274bp
        0.1M
        m45_R1
        93.8%
        46%
        284bp
        0.1M
        m45_R2
        83.8%
        44%
        274bp
        0.1M
        m46_R1
        93.2%
        45%
        284bp
        0.0M
        m46_R2
        81.9%
        43%
        274bp
        0.0M
        m4_R1
        93.8%
        45%
        284bp
        0.0M
        m4_R2
        84.4%
        43%
        274bp
        0.0M
        m5_R1
        96.7%
        46%
        284bp
        0.6M
        m5_R2
        90.3%
        43%
        274bp
        0.6M
        m6_R1
        97.3%
        47%
        284bp
        0.1M
        m6_R2
        88.4%
        45%
        274bp
        0.1M
        m7_R1
        96.3%
        45%
        284bp
        0.2M
        m7_R2
        91.0%
        42%
        274bp
        0.2M
        m8_R1
        95.0%
        45%
        284bp
        0.1M
        m8_R2
        87.6%
        43%
        274bp
        0.1M
        m9_R1
        93.9%
        46%
        284bp
        0.0M
        m9_R2
        81.7%
        45%
        274bp
        0.0M
        neg1_R1
        81.3%
        71%
        34bp
        0.0M
        neg1_R2
        79.9%
        83%
        34bp
        0.0M
        neg2_R1
        82.9%
        63%
        34bp
        0.0M
        neg2_R2
        83.8%
        83%
        34bp
        0.0M
        s12428_R1
        94.5%
        46%
        284bp
        0.0M
        s12428_R2
        86.0%
        44%
        274bp
        0.0M
        s12430_R1
        95.9%
        45%
        284bp
        0.1M
        s12430_R2
        86.0%
        43%
        274bp
        0.1M
        s12438_R1
        98.1%
        46%
        284bp
        0.5M
        s12438_R2
        91.4%
        44%
        274bp
        0.5M
        s12614_R1
        98.5%
        44%
        284bp
        0.5M
        s12614_R2
        93.1%
        42%
        274bp
        0.5M
        s12884_R1
        95.8%
        46%
        284bp
        0.1M
        s12884_R2
        83.4%
        45%
        274bp
        0.1M
        s12903_R1
        97.5%
        45%
        284bp
        0.5M
        s12903_R2
        91.0%
        43%
        274bp
        0.5M
        s138530_R1
        95.7%
        47%
        284bp
        0.1M
        s138530_R2
        88.8%
        44%
        274bp
        0.1M
        s15825_R1
        81.4%
        48%
        284bp
        0.0M
        s15825_R2
        69.3%
        46%
        274bp
        0.0M
        s15827_R1
        84.5%
        47%
        284bp
        0.0M
        s15827_R2
        72.2%
        45%
        274bp
        0.0M
        s15829_R1
        78.0%
        46%
        284bp
        0.0M
        s15829_R2
        61.2%
        45%
        274bp
        0.0M
        s15947_R1
        97.1%
        45%
        284bp
        0.1M
        s15947_R2
        88.1%
        43%
        274bp
        0.1M
        s15949_R1
        97.6%
        45%
        284bp
        0.1M
        s15949_R2
        88.8%
        43%
        274bp
        0.1M
        s15965_R1
        97.6%
        45%
        284bp
        0.2M
        s15965_R2
        89.6%
        43%
        274bp
        0.2M
        s15981_R1
        92.7%
        44%
        284bp
        0.0M
        s15981_R2
        81.7%
        42%
        274bp
        0.0M
        s15987_R1
        97.4%
        46%
        284bp
        0.2M
        s15987_R2
        90.3%
        44%
        274bp
        0.2M
        s15997_R1
        94.9%
        44%
        284bp
        0.0M
        s15997_R2
        83.2%
        42%
        274bp
        0.0M
        s16001_R1
        97.4%
        46%
        284bp
        0.2M
        s16001_R2
        91.2%
        43%
        274bp
        0.2M
        s19481_R1
        97.6%
        46%
        284bp
        0.3M
        s19481_R2
        89.8%
        43%
        274bp
        0.3M
        s19501_R1
        94.3%
        46%
        284bp
        0.1M
        s19501_R2
        85.4%
        44%
        274bp
        0.1M
        s19505_R1
        93.0%
        46%
        284bp
        0.1M
        s19505_R2
        84.6%
        44%
        274bp
        0.1M
        s19507_R1
        90.1%
        46%
        284bp
        0.0M
        s19507_R2
        75.3%
        44%
        274bp
        0.0M
        s19509_R1
        86.3%
        47%
        284bp
        0.0M
        s19509_R2
        72.8%
        46%
        274bp
        0.0M
        s19511_R1
        97.5%
        49%
        284bp
        0.1M
        s19511_R2
        88.5%
        46%
        274bp
        0.1M
        s19594_R1
        92.5%
        47%
        284bp
        0.0M
        s19594_R2
        84.2%
        45%
        274bp
        0.0M
        s39300_R1
        81.2%
        49%
        284bp
        0.0M
        s39300_R2
        70.9%
        47%
        274bp
        0.0M
        s39314_R1
        86.1%
        49%
        284bp
        0.0M
        s39314_R2
        76.9%
        47%
        274bp
        0.0M
        s39326_R1
        95.8%
        43%
        284bp
        0.1M
        s39326_R2
        89.3%
        41%
        274bp
        0.1M
        s39352_R1
        87.7%
        46%
        284bp
        0.0M
        s39352_R2
        77.9%
        45%
        274bp
        0.0M
        s401612_R1
        94.0%
        45%
        284bp
        0.1M
        s401612_R2
        86.0%
        43%
        274bp
        0.1M
        s401614_R1
        89.9%
        45%
        284bp
        0.0M
        s401614_R2
        79.0%
        42%
        274bp
        0.0M
        s401616_R1
        89.5%
        46%
        284bp
        0.0M
        s401616_R2
        79.7%
        43%
        274bp
        0.0M
        s401618_R1
        88.1%
        46%
        284bp
        0.0M
        s401618_R2
        78.7%
        43%
        274bp
        0.0M
        s401620_R1
        89.6%
        47%
        284bp
        0.0M
        s401620_R2
        78.5%
        44%
        274bp
        0.0M
        s401622_R1
        94.1%
        46%
        284bp
        0.1M
        s401622_R2
        83.9%
        43%
        274bp
        0.1M
        s401632_R1
        86.1%
        47%
        284bp
        0.0M
        s401632_R2
        78.3%
        45%
        274bp
        0.0M
        s401634_R1
        89.5%
        46%
        284bp
        0.0M
        s401634_R2
        77.9%
        45%
        274bp
        0.0M
        s401644_R1
        87.8%
        46%
        284bp
        0.0M
        s401644_R2
        74.0%
        44%
        274bp
        0.0M
        s401646_R1
        89.9%
        47%
        284bp
        0.0M
        s401646_R2
        80.9%
        45%
        274bp
        0.0M
        s401650_R1
        80.2%
        48%
        284bp
        0.0M
        s401650_R2
        72.1%
        47%
        274bp
        0.0M
        s401652_R1
        96.8%
        44%
        284bp
        0.3M
        s401652_R2
        90.2%
        41%
        274bp
        0.3M
        s401654_R1
        97.6%
        47%
        284bp
        0.1M
        s401654_R2
        90.3%
        43%
        274bp
        0.1M
        s401656_R1
        98.0%
        47%
        284bp
        0.2M
        s401656_R2
        92.4%
        44%
        274bp
        0.2M
        s401658_R1
        85.8%
        45%
        284bp
        0.0M
        s401658_R2
        64.4%
        44%
        274bp
        0.0M
        s401660_R1
        97.3%
        47%
        284bp
        0.2M
        s401660_R2
        90.3%
        45%
        274bp
        0.2M
        s401954_R1
        95.8%
        44%
        284bp
        0.1M
        s401954_R2
        85.1%
        43%
        274bp
        0.1M
        s401956_R1
        85.5%
        46%
        284bp
        0.0M
        s401956_R2
        72.6%
        43%
        274bp
        0.0M
        s401964_R1
        97.5%
        45%
        284bp
        0.1M
        s401964_R2
        90.5%
        43%
        274bp
        0.1M
        s401972_R1
        92.9%
        45%
        284bp
        0.1M
        s401972_R2
        83.3%
        44%
        274bp
        0.1M
        s401974_R1
        97.6%
        44%
        284bp
        0.3M
        s401974_R2
        89.7%
        42%
        274bp
        0.3M
        s401978_R1
        96.6%
        44%
        284bp
        0.1M
        s401978_R2
        81.3%
        43%
        274bp
        0.1M
        s401996_R1
        95.6%
        46%
        284bp
        0.1M
        s401996_R2
        87.4%
        45%
        274bp
        0.1M
        s402006_R1
        93.9%
        47%
        284bp
        0.0M
        s402006_R2
        81.9%
        46%
        274bp
        0.0M
        s402112_R1
        96.0%
        46%
        284bp
        0.1M
        s402112_R2
        85.4%
        44%
        274bp
        0.1M
        s402116_R1
        88.0%
        46%
        284bp
        0.0M
        s402116_R2
        82.2%
        44%
        274bp
        0.0M
        s402118_R1
        86.9%
        45%
        284bp
        0.0M
        s402118_R2
        73.1%
        43%
        274bp
        0.0M
        s402120_R1
        89.8%
        45%
        284bp
        0.0M
        s402120_R2
        79.5%
        43%
        274bp
        0.0M
        s402122_R1
        87.2%
        47%
        284bp
        0.0M
        s402122_R2
        76.9%
        45%
        274bp
        0.0M
        s402124_R1
        90.1%
        45%
        284bp
        0.0M
        s402124_R2
        81.5%
        44%
        274bp
        0.0M
        s402150_R1
        92.4%
        44%
        284bp
        0.0M
        s402150_R2
        80.9%
        42%
        274bp
        0.0M
        s62120_R1
        92.2%
        45%
        284bp
        0.0M
        s62120_R2
        80.1%
        44%
        274bp
        0.0M
        s62128_R1
        97.6%
        48%
        284bp
        0.2M
        s62128_R2
        91.7%
        44%
        274bp
        0.2M
        s62134_R1
        85.3%
        50%
        284bp
        0.0M
        s62134_R2
        78.1%
        48%
        274bp
        0.0M
        s62150_R1
        92.8%
        45%
        284bp
        0.1M
        s62150_R2
        83.1%
        44%
        274bp
        0.1M
        s62152_R1
        92.6%
        45%
        284bp
        0.1M
        s62152_R2
        84.5%
        44%
        274bp
        0.1M
        s62154_R1
        98.3%
        41%
        284bp
        0.2M
        s62154_R2
        94.0%
        38%
        274bp
        0.2M
        s62156_R1
        93.0%
        45%
        284bp
        0.1M
        s62156_R2
        84.1%
        43%
        274bp
        0.1M
        s62158_R1
        93.8%
        45%
        284bp
        0.1M
        s62158_R2
        85.3%
        43%
        274bp
        0.1M
        s62160_R1
        91.9%
        46%
        284bp
        0.1M
        s62160_R2
        84.3%
        44%
        274bp
        0.1M
        s62162_R1
        95.3%
        43%
        284bp
        0.1M
        s62162_R2
        86.7%
        42%
        274bp
        0.1M
        s62164_R1
        92.1%
        46%
        284bp
        0.0M
        s62164_R2
        83.5%
        44%
        274bp
        0.0M
        s62166_R1
        91.7%
        46%
        284bp
        0.0M
        s62166_R2
        80.6%
        44%
        274bp
        0.0M
        s62168_R1
        92.8%
        45%
        284bp
        0.0M
        s62168_R2
        84.7%
        43%
        274bp
        0.0M
        s62170_R1
        89.8%
        47%
        284bp
        0.0M
        s62170_R2
        81.1%
        45%
        274bp
        0.0M
        s62172_R1
        90.2%
        47%
        284bp
        0.0M
        s62172_R2
        81.6%
        45%
        274bp
        0.0M
        s62174_R1
        89.7%
        47%
        284bp
        0.0M
        s62174_R2
        81.6%
        45%
        274bp
        0.0M
        s7839_R1
        88.2%
        44%
        284bp
        0.0M
        s7839_R2
        68.9%
        42%
        274bp
        0.0M
        s7857_R1
        98.7%
        46%
        284bp
        0.5M
        s7857_R2
        92.7%
        44%
        274bp
        0.5M
        s7863_R1
        94.2%
        45%
        284bp
        0.1M
        s7863_R2
        84.1%
        42%
        274bp
        0.1M
        s9450_R1
        93.3%
        47%
        284bp
        0.1M
        s9450_R2
        86.2%
        44%
        274bp
        0.1M
        s9466_R1
        91.7%
        44%
        284bp
        0.0M
        s9466_R2
        76.8%
        42%
        274bp
        0.0M
        s9586_R1
        94.5%
        45%
        284bp
        0.1M
        s9586_R2
        87.3%
        43%
        274bp
        0.1M

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        CCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACC
        126
        2342675
        7.3417%
        CCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAATT
        126
        2751946
        8.6243%
        CCAGTAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATT
        126
        304221
        0.9534%
        CCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATT
        126
        344995
        1.0812%
        CCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACT
        126
        1358023
        4.2559%
        CCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATT
        126
        548684
        1.7195%
        CCAATAGCGTATATTAAAATTGTTGCAGTTAAAAAGCTCGTAGTTGGATT
        126
        198582
        0.6223%
        CATAAGGTGCGAATGAAGTCGAAAATGCAACGTTCACTCATCCCTAGTCG
        126
        329103
        1.0314%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        126
        81564
        0.2556%
        CCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATC
        125
        1078955
        3.3813%
        CATAAGGTGCCAAACAAGTCAAAATATCCTTGCCTGATCCCTAGTCGGCA
        123
        487993
        1.5293%
        CGTAAGGTGCCGAACGGGTCATCATAGAATCCCGTCCGATCCCTAGTCGG
        122
        352904
        1.1060%
        CCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTCGAATT
        120
        89075
        0.2792%
        CCAATAGCGTATACTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAATT
        118
        61848
        0.1938%
        CCAATAGCGTATATTAAAGTTGTTGTGGTTAAAAAGCTCGTAGTTGAACC
        116
        95582
        0.2995%
        NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
        116
        15447
        0.0484%
        CCAAGAGCATATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATT
        115
        54190
        0.1698%
        CATAAGGTGCGGATGAAGTCGAAAATGCAACGTTCACCCATCCCTAGTTG
        115
        60855
        0.1907%
        CCAATAGCGTATATTAAAGTTGTTGCCGTTAAAAAGCTCGTAGTTGAACC
        114
        816615
        2.5592%
        CATAAGGTGCCAAACAAGTCAAAAAATCCTTGTCTGATCCCTAGTCGGCA
        113
        237575
        0.7445%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1